Contacts of the helix formed by residues 84 - 96 (chain E) in PDB entry 1L3R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 84 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54E PHE* 3.4 34.6 - - + -
79E VAL* 2.9 22.3 + - + +
82E LEU* 2.9 27.0 + - + +
83E LYS* 1.3 86.8 + - - +
85E ILE* 1.3 58.0 + - - +
86E GLU 3.5 1.6 - - - -
87E HIS* 2.8 37.2 + - + +
88E THR* 2.7 41.7 + - - +
187E PHE* 3.4 14.0 - - - -
23I HIS* 3.5 23.6 - - - +
24I ASP* 5.2 0.8 - - - +
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Residues in contact with ILE 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E VAL* 3.9 6.1 - - - -
80E VAL* 3.8 47.1 - - + +
83E LYS* 3.5 4.3 + - - -
84E GLN* 1.3 79.9 - - - +
86E GLU* 1.3 65.4 + - - +
88E THR* 3.2 2.8 + - - -
89E LEU* 3.2 28.7 + - + +
346E GLU* 3.9 39.7 - - + +
347E PHE* 4.0 14.9 - - + -
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Residues in contact with GLU 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E LYS 5.5 0.2 + - - -
84E GLN 3.5 0.2 - - - -
85E ILE* 1.3 79.3 - - - +
87E HIS* 1.3 61.9 + - + +
89E LEU* 3.3 20.6 + - - +
90E ASN* 2.9 51.8 + - - +
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Residues in contact with HIS 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E LYS 5.1 4.2 + - - -
84E GLN* 2.8 43.5 + - + +
85E ILE 3.2 0.6 - - - -
86E GLU* 1.3 83.0 - - + +
88E THR* 1.3 58.0 + - - +
90E ASN* 3.3 17.1 + - - +
91E GLU* 2.8 23.6 + - - +
165E ARG* 3.7 9.3 + - - -
186E GLY 3.3 25.4 - - - +
187E PHE* 3.7 16.2 - + - -
197E TPO 2.7 51.5 + - + +
199E CYS* 4.4 6.1 - - + -
23I HIS* 6.2 0.4 - - + -
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Residues in contact with THR 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E LEU* 3.9 18.6 - - + +
79E VAL* 3.5 17.2 - - + +
84E GLN* 2.7 26.3 + - - +
85E ILE 3.6 3.8 - - - -
87E HIS* 1.3 74.6 - - - +
89E LEU* 1.3 65.8 + - - +
91E GLU* 3.4 12.9 + - - +
92E LYS* 3.2 23.2 + - - +
116E LEU* 3.4 33.0 - - + -
118E MET* 5.3 0.4 - - + -
347E PHE* 4.5 2.9 - - + -
350E PHE* 4.3 9.8 - - + -
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Residues in contact with LEU 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E ILE* 3.2 20.5 + - + +
86E GLU* 3.7 25.1 - - - +
87E HIS 3.3 0.2 - - - -
88E THR* 1.3 72.7 - - - +
90E ASN* 1.3 66.5 + - - +
92E LYS* 4.1 4.1 - - - +
93E ARG* 3.0 27.9 + - - +
346E GLU 4.0 15.5 - - - +
347E PHE* 4.2 18.6 - - + -
349E GLU* 3.8 40.5 - - + +
350E PHE* 4.1 24.9 - - + +
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Residues in contact with ASN 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E TRP* 5.5 6.1 - - - -
86E GLU* 2.9 38.2 + - - +
87E HIS* 3.4 23.5 - - - +
88E THR 3.3 0.2 - - - -
89E LEU* 1.3 76.7 - - - +
91E GLU* 1.3 54.7 + - - +
93E ARG* 4.6 4.4 - - - +
94E ILE* 2.8 47.3 + - + +
188E ALA 3.3 24.0 + - - +
189E LYS* 4.1 23.3 - - - +
190E ARG 5.5 1.3 + - - -
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Residues in contact with GLU 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E LYS* 2.8 30.5 + - - +
74E LEU* 4.3 6.8 - - - +
87E HIS 2.8 16.0 + - - +
88E THR* 3.5 15.3 + - - +
90E ASN* 1.3 76.8 - - - +
92E LYS* 1.3 57.4 + - - +
94E ILE* 4.1 1.0 - - - +
95E LEU* 3.0 36.6 + - + +
118E MET* 3.4 28.2 - - - +
184E ASP* 4.8 0.7 - - - -
185E PHE* 3.5 36.9 + - + +
186E GLY* 3.4 19.5 + - - -
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Residues in contact with LYS 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E PRO* 4.4 11.3 - - - +
34E SER 2.9 26.4 + - - +
35E GLN* 4.4 1.2 - - - +
88E THR 3.2 7.0 + - - +
89E LEU* 4.2 2.0 - - - +
91E GLU* 1.3 76.7 - - - +
93E ARG* 1.3 66.6 + - - +
95E LEU* 4.2 2.1 - - - +
96E GLN* 3.0 39.5 + - + +
106E LEU* 4.2 3.7 - - + +
109E SER* 4.0 21.2 + - - +
118E MET* 4.2 14.1 - - + -
349E GLU 3.9 9.8 + - - -
350E PHE* 3.1 73.2 + - + +
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Residues in contact with ARG 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E TRP* 3.0 77.5 + - + +
31E GLU* 4.5 10.5 + - - +
33E PRO* 3.9 21.2 - - + +
89E LEU 3.0 19.4 + - - +
90E ASN* 3.9 4.3 - - - +
92E LYS* 1.3 82.1 - - - +
94E ILE* 1.3 62.1 + - - +
96E GLN* 2.7 31.9 + - - +
97E ALA* 3.6 4.2 - - - +
349E GLU* 4.2 22.1 + - - +
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Residues in contact with ILE 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E PHE* 4.7 3.4 - - + -
30E TRP* 4.0 20.6 - - + -
90E ASN* 2.8 29.5 + - + +
91E GLU 4.1 1.3 - - - +
93E ARG* 1.3 72.1 - - - +
95E LEU* 1.3 64.1 + - - +
97E ALA* 3.0 14.4 + - - +
98E VAL* 3.1 15.7 + - + +
162E LEU* 3.7 39.5 - - + -
185E PHE* 3.8 22.7 - - + -
188E ALA* 3.5 35.2 - - + +
189E LYS* 3.6 11.9 - - - +
190E ARG 3.9 3.1 - - - +
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Residues in contact with LEU 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E GLU* 3.0 22.8 + - + +
92E LYS* 4.2 2.7 - - - +
94E ILE* 1.3 78.8 - - - +
96E GLN* 1.3 60.6 + - - +
97E ALA 3.1 1.3 + - - -
98E VAL* 3.6 23.4 + - + +
103E LEU* 5.8 0.4 - - + -
104E VAL* 3.5 32.2 - - + +
106E LEU* 3.8 37.7 + - + +
118E MET* 5.0 10.8 - - + -
120E MET* 4.5 17.0 - - + -
184E ASP 6.0 1.1 - - - +
185E PHE* 4.1 34.5 - - + +
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Residues in contact with GLN 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E LYS* 3.1 42.9 + - - +
30E TRP* 4.2 1.2 - - - +
32E THR 4.6 0.3 - - - +
33E PRO* 3.3 20.1 - - + +
34E SER* 3.0 34.6 + - - +
92E LYS* 3.0 36.4 + - + +
93E ARG* 2.7 22.2 + - - +
95E LEU* 1.3 75.8 - - - +
97E ALA* 1.3 66.3 + - - +
98E VAL 3.8 1.6 - - - +
106E LEU* 3.7 22.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il